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Combining 7T T2 and 3T FGATIR: from physiological to anatomical identification of the subthalamic nucleus borders
  1. Niels Rijks1,
  2. Wouter V Potters2,
  3. José Dilai2,
  4. Rob M A De Bie2,
  5. Maartje de Win3,
  6. Wietske van der Zwaag4,
  7. Richard Schuurman1,
  8. Pepijn van den Munckhof1,
  9. Maarten Bot1
  1. 1 Department of Neurosurgery, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
  2. 2 Department of Neurology and Clinical Neurophysiology, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
  3. 3 Department of Radiology and Nuclear Medicine, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
  4. 4 Royal Netherlands Academy of Arts and Sciences, Spinoza Centre for Neuroimaging, Amsterdam, The Netherlands
  1. Correspondence to Niels Rijks, Department of Neurosurgery, Amsterdam UMC Location AMC, Amsterdam, The Netherlands; n.h.rijks{at}

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Both 7-Tesla (7T) and 3-Tesla (3T) MRI sequences can be used for identification of the subthalamic nucleus (STN) in deep brain stimulation (DBS) for Parkinson’s disease.1

On our 7T T2 sequence the dorsal STN-border is clearly shown but the ventral STN border cannot be distinguished sufficiently from the substantia nigra (SN).1 The 3T Fast Grey Matter Acquisition T1 Inversion Recovery (FGATIR) and other 3T sequences offer a clear contrast between the ventral border of the STN and the SN2

Several publications have found excellent correlation between the MR-visualised STN and microelectrode recordings (MER). Here, we present a novel combination of 7T T2 (dorsal border) and 3T FGATIR MRI (ventral border) which also accomplishes this aim.



Data were collected from all patients undergoing DBS surgery at our institution between November 2019 and October 2020 in whom 7T T2 and 3T FGATIR MRI were available in addition to the standard 3T T1 and T2 sequences used for DBS planning.

All patients gave consent for the extra 7T T2 MRI and 3T FGATIR sequence acquisition.

Image acquisition and surgical procedure

The extra MRI sequences were: (1) 7T 3D T2-weighted and (2) 3T 3D FGATIR. Stereotactic registration and electrode localisation were done using intraoperative CT. See online supplemental methods for imaging parameters and surgical procedure.3

Supplemental material


STN borders determined by MER

MERs were started 6 mm above the calculated target and advanced with 0.5 mm steps until the electrophysiological STN signal ended. The central MER trajectories were used in the analyses. Electrophysiological activity of the STN were recognised as a typical broadening of background signal with tonic and irregular discharge patterns and occasional bursts. The ventral border was marked by the disappearance of this typical pattern. The dorsal and ventral electrophysiological STN borders were expressed in millimetre distance to the calculated target

STN borders determined by 7T T2 and 3T FGATIR MRI

STN border identification on 7T T2 and 3T FGATIR was done …

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  • Contributors NR, MB, PvdM and RS have overseen the main writing of this article and implementing of the MRI sequences. WvdZ and MdW have overseen MRI techniques and details. JD and WVP have overseen the electrophysiological matters. RMADB has overseen the neurological theory.

  • Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.

  • Competing interests None declared.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.